MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vqo:08005, See in JSmolClick on the image to toggle views Site type: mer-3Oph Schematic drawing for mer-3Oph List of all 430 Mg2+ binding sites with the site type mer-3Oph in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 7 of 18 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ccr 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03618, 07774, 07775 G:01837 U:01835 A:01839 3ccr 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03637, 07767, 07848 G:02466, C:0920, G:02293 3ccq 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03632, 07829, 07830 G:01837 U:01835 A:01839 3ccm 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03640, 07813, 07814 G:01837 A:01839 3ccl 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03654, 07800, 07882 G:02466, C:0920, G:02293 3ccl 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03635, 07807, 07808 G:01837 A:01839 3ccj 08084 mer-3Oph C:01103(OP1), A:01106(OP2), A:01107(OP2) 07788, 07789, 07790 C:01104 A:01107 3cce 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03651, 07797, 07880 G:02466, C:0920 3cce 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03633, 07804, 07805 G:01837 U:01835 A:01839 3cc7 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03664, 07823, 07905 G:02466, C:0920, G:02293 3cc7 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03645, 07830, 07831 G:01837 U:01835 A:01839 3cc2 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03165, 07341, 07342 G:01837 A:01839 3cc2 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07330, 08529, 09903 G:0833 3cc2 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03657, 09146 3cc2 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03183, 07334, 07417 G:02466, G:02293 3b4c B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B402, A401 G:A1, A:B35 3b4b B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B403, B404, B405 G:A1 3b4a B201 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A301, A302, B303 G:A3 G:A1, A:B35 2z75 B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A401, B402, B465 G:A1, A:B35 2z4n B2943 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3202, B3203, B3204 A:B947 2z4n B2991 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3423, B3424, B3425 U:B1781 2z4n B2993 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3429, B3430, B3431 U:B741 2z4n B2945 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3210, B3211, B3212 A:B2430 2z4n B3010 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3492, B3493, B3494 2z4m A1545 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1610, A1611, A1612 U:A571

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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